softparsmap
Class TreeParserNewick

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.AbstractTreeParser
          softparsmap.TreeParserNewick

All Implemented Interfaces:

Dependencies, TreeParser

public class TreeParserNewick

extends AbstractTreeParser

This parser will parse the Newick format. It is flexible within limits, See the def.xml file for more information.

Constructor Summary

TreeParserNewick()

Method Summary

EdgeType	getEdgeType() Returns the edge type that exists in the tree.
void	parseIn(Node tree, java.lang.String treeInfo) Adding information to the existing tree.
Node	parseIn(java.lang.String tree) Returns the root of the parsed tree.
java.lang.String	parseOut(Node tree) This method will parse out the tree to a string.
void	setEdgeType(EdgeType edgeType)
void	setupInstance() The default setup method which will be called.

Methods inherited from class softparsmap.AbstractTreeParser

getCharset, getPropertyFile, parseIn, parseIn, parseOut

Methods inherited from class ooc.LinkedTagInstance

containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TreeParserNewick

public TreeParserNewick()

Method Detail

setupInstance

public void setupInstance()

Description copied from class: LinkedTagInstance

The default setup method which will be called.

Overrides:

setupInstance in class LinkedTagInstance

getEdgeType

public EdgeType getEdgeType()

Returns the edge type that exists in the tree. It is defined by the attribute 'edge_type' in the tag.

Returns:

an edge type

See Also:

EdgeType

setEdgeType

public void setEdgeType(EdgeType edgeType)

parseIn

public Node parseIn(java.lang.String tree)

Description copied from interface: TreeParser

Returns the root of the parsed tree. The tree is parsed from a string.

Specified by:

parseIn in interface TreeParser

Specified by:

parseIn in class AbstractTreeParser

parseOut

public java.lang.String parseOut(Node tree)

Description copied from interface: TreeParser

This method will parse out the tree to a string.

Specified by:

parseOut in interface TreeParser

Specified by:

parseOut in class AbstractTreeParser

parseIn

public void parseIn(Node tree,
                    java.lang.String treeInfo)

Description copied from interface: TreeParser

Adding information to the existing tree. The parser extracts the node information and adds it to the relevent node by mapping the key to the node information in the relevent node map.

Specified by:

parseIn in interface TreeParser

Specified by:

parseIn in class AbstractTreeParser